Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Mills, James E.; Dean, Philip M.

doi:10.1007/bf00134183

Cited by 249 publications

(231 citation statements)

References 40 publications

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“…Compounds can also be screened by the number of hydrogen bonds formed with the target structure and by whether or not the hydrogen bonds involve specified groups in the site. Hydrogen-bond detection uses a set of detailed distance and angle criteria from a published small-molecule crystal survey 25 and is an extension-provided capability of Chimera.…”

Section: Viewdockmentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

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Abstract:The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from

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Section: Viewdockmentioning

confidence: 99%

UCSF Chimera—A visualization system for exploratory research and analysis

et al. 2004

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“…Ligand atoms, which are capable of forming hydrogen bridges, are identified as anchor atoms according to the procedure introduced by Mills and Dean. [10] 4. Grid points with valid hydrogen bonding constraints are declared as pseudoatoms with a pharmacophoric feature that is complementary to the respective anchor atom.…”

Section: Pseudoreceptor Construction Methodsmentioning

confidence: 99%

“…They are positioned according to hydrogen bond constraints found in a crystal survey of the Protein Data Bank (PDB). [10] PRPS pseudoreceptor generation consists of four steps: 1) grid assembly, 2) deletion of invalid points, 3) identification of PPPs, and 4) pseudoatom projection. The procedural method is to pinpoint putative receptor atom positions by selecting valid grid points as pseudoatoms.…”

Section: Pseudoreceptor Construction Methodsmentioning

confidence: 99%

Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H₄ Receptor

et al. 2009

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A computer-assisted method for the generation of pseudoreceptor models is presented together with two practical applications. From a three-dimensional alignment of known histamine H(4) receptor ligands, a pseudoreceptor model of the putative ligand binding site was constructed and used for virtual screening of a large collection of commercially available compounds. Two bioactive chemotypes were retrieved, demonstrating the general applicability of the approach. The pseudoreceptor model was also used to find the putative ligand binding pocket within the transmembrane receptor domain. For each frame of a molecular dynamics simulation of a homology-based H(4) receptor model, we automatically extracted potential ligand binding pockets and used their compatibility with the pseudoreceptor as a selection criterion. The best-matching pocket fits perfectly with existing mutation data and previously published hypotheses suggesting Glu182(5.46) as the preferred binding partner of a positively charged moiety of H(4) receptor ligands. This new pseudoreceptor approach has demonstrated its suitability for both structure-based prioritization of protein receptor models, and ligand-based virtual screening with the aim to perform scaffold hopping.

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“…To determine the parts of the binding system that strongly interacted with other molecules, the H-bonds between POT1 and telomeric ssDNA were investigated. To this end, the three-dimensional geometrical-based hydrogen (H)-bond criteria 34 were used. These criteria are based on the angle and distance between an acceptor (A) and donor (D) pair.…”

Section: Root-mean-square Fluctuationmentioning

confidence: 99%

Molecular dynamics simulation of telomeric single-stranded DNA and POT1

Kaburagi

Yamada

Miyakawa

et al. 2015

Polym J

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Telomeres, which consist of single-, double-and four-stranded DNA, shorten after each round of cell division. The repeated telomeric DNA sequence 5′-TTAGGG-3′ does not encode genetic information and is not replicated completely. We performed molecular dynamics (MD) simulations of telomeric single-stranded DNA (ssDNA) and protection of telomere 1 (POT1) for 100 ns. We calculated the distance between C α (POT1) and O5' (telomeric ssDNA) to verify the binding system for 100 ns MD. We then calculated the distance between the bases of the telomeric DNA ends and the root-mean-square deviation and gyration radius in the single and binding states. Moreover, we compared the root-mean-square fluctuations (RMSFs) between the single and binding states and calculated the number of hydrogen bonds between POT1 and telomeric DNA. There are many hydrogen bonds between Gln94 and the first guanine of the closest 5′-TTAGGG-3′ sequence in telomeric single-stranded DNA, and the RMSF between the single and binding states has a large difference between Gln94 and guanine. Overall, we found that Gln94 and guanine are important components of the binding system and are related to the stability of this system.

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Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Cited by 249 publications

References 40 publications

UCSF Chimera—A visualization system for exploratory research and analysis

UCSF Chimera—A visualization system for exploratory research and analysis

Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H₄ Receptor

Molecular dynamics simulation of telomeric single-stranded DNA and POT1

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Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Cited by 249 publications

References 40 publications

UCSF Chimera—A visualization system for exploratory research and analysis

UCSF Chimera—A visualization system for exploratory research and analysis

Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H4 Receptor

Molecular dynamics simulation of telomeric single-stranded DNA and POT1

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Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H₄ Receptor